Chanalyzer: a computational geometry approach for the analysis of protein channel shape and dynamics
This repository contains the routines behind the paper [1]. The repository is organized in four sub-folders:
- Step A: extraction of the tetrahedral representation of the channel.
- Step B: channel projection onto the SES generated via NanoShaper.
- Step C1: skeletonization.
- Step C2: extraction of source and target points.
- Step D1: centerline computation and geometry processing.
- Step D2: extraction and analysis of channel's sections.
A graphical abstract representing this pipeline is given in the following figure (note that C1 and C2 are summarized as a single step C; similarly, D1 and D2 are summed up as step D):
Updates can be roughly classified into three main contributions:
- the introduction of a new step (Step E) aimed at providing new metrics for the retrieved channel and new visual representations of it;
- a modified pipeline (including new steps and programs) to deal with occluded channels;
- a modified pipeline (including new steps and programs) if a pathway is provided as input.
Please check the README files of the corresponding folders to learn more.
The datasets analyzed for this study and the configuration parameter file for NanoShaper calculation can be found in the Zenodo repository, DOI: 10.5281/zenodo.6509652.
A script to convert a trajectory from the multiple pdb format to the frames that compose it in xyzr format is provided in https://github.com/concept-lab/mpdb2xyzr.git.
[1] A. Raffo, L. Gagliardi, U. Fugacci, L. Sagresti, S. Grandinetti, G. Brancato S. Biasotti, W. Rocchia. "Chanalyzer: a computational geometry approach for the analysis of protein channel shape and dynamics". Frontiers in Molecular Biosciences 9:933924, 2022. doi: 10.3389/fmolb.2022.933924
[2] S. Decherchi, W. Rocchia. "A general and Robust Ray-Casting-Based Algorithm for Triangulating Surfaces at the Nanoscale". PLOS ONE 8(4): e59744, 2013.